Code Lyoko: Krystal is Back
by Ayami55
Summary: After shutting down the super computer for a few months, it's now a new school year for the Lyoko Warriors. Everything is peaceful, but what happens when a mysterious boy turns on the super computer? And who are these new transfer students? How does Krystal's past tie in to all of this? Sequel to Code Lyoko: Code Krystal
1. Prologue

**IMPORTANT NOTE:**

 **MY OCs LOOK LIKE THE PEOPLE ON THE STORY COVER** **(As usual)**

 **Author's note: And here is the prologue! I'm warning you, this may be:**

 **Short**

 **Bad**

 **Just Un-readable**

 **Because I am fairly bad at prologues, so read at your own cost. ;3**

* * *

 _It was Sunday night, getting ready for Monday, a young boy, probably no older than 14, was running to the entrance of the forest. He kept on running until he saw a certain sewer hole, jumping in it, he raced down in the sewer, trying to find a ladder. Once he found the ladder, he climbed up and out of the sewer, running towards a certain factory. He pushed the elevator button and suddenly, the elevator doors opened. Stepping in, he then pushed the down button and the elevator was taking him down a floor._

 _Once the elevator doors opened, the boy stepped into a room, where the super computer's power was. He walked over to the lever, which was currently facing down. He pulled the lever up and the super computer started to glow. The boy smiled as he saw this._

 _"I'd better get back..." The boy muttered, looking at his phone, as it was currently 4:00 in the morning. He rushed up to the super computer and started to type in random things, trying to get the super computer's screen to turn on. When the screen turned on, it revealed a certain eye symbol, the computer then said "Loading 67%"_

 _"Yes!" The boy exclaimed, he then got onto the elevator and left the room, once the computer stopped loading, it then went blank again._

 _After about a couple of hours, the scanner doors opened to reveal a boy, who looked a little bit like 15(Yumi and William's age.. right?). He groaned as he opened his brown eyes to see that he was in the scanner room._

 _"Yes... it worked!" He shouted, getting out of the scanner, he then went to the super computer, where it showed a reflection of himself, he looked up at his blonde hair in confusion._

 _"I thought my hair was black.. hmm... Maybe I accidently used too much of that Odd kid's human signature.." He mumbled, turning the super computer's screen on. The young boy typed in a few codes and commands and after about several minutes, a girl appeared on the screen. She had beautiful blonde hair and blue/purplish eyes._

 _She looked around and saw the blonde haired boy, who was staring blankly at her._

 _"W-who are you..?" She finally spoke, the blonde boy raised one of his eye brows._

 _"That's not important." The boy replied, still staring blankly at her. The girl looked confused at the response._

 _"Then.. who am I?" She asked, but the boy once again stared at her blankly and began to type some codes in, repeating, "That's not important."_

 _Becoming slightly annoyed, the girl asked, "Then what is important?"_

 _Looking up from the keyboard, the boy looked up at her, once again blankly and simply stating, "Getting you to here."_

 _"Where's 'here'" The girl once again asked._

 _The boy, instead of answering what she asked, said, "Due to the super computer being down for some time, some of your human signatures are lost, I'll have to make some artificial ones to materialize you here."_

 _"Where's 'here'" She repeated once again, and the boy did not answer, he instead, was still looking down at the keyboard, typing in some codes._

 _"Ya know, for a cute boy, you sure are rude." She noted, putting her lips into a pout._

 _He looked up at her and remarked, "And for a cute girl, you sure are talkative, now stay quiet, I am trying to focus. Unless, you want to be trapped in that tower forever."_

 _On the other side of the screen, the girl looked around to see that she was trapped in a tower(a normal Lyoko tower). Sighing in defeat, she replied, "Alright.. alright.. I'll wait."_

 _The boy smiled hearing this from her lips and saying, "Good, I'll explain everything to you once you get out." Now the boy did smile because he had a plan, a plan to destroy the Lyoko warriors once in for all. They were too much of a threat for him to rule the world, and the boy was especially happy because now, he has a ally to help him._

 _He pressed the 'enter' button and the screen went blank. Furrowing his eye brows as the scene, he got off of the chair and ran to the scanner room, there, he saw a young girl, with blue hair into a side ponytail, unconscious. After a few seconds, the girl's eyes opened, revealing bluish/green in her eyes. She slowly got up, with a little bit of the boy's help, and stood right infront of him, staring intensely in his eyes._

 _"So. Who. Am. I.?" The girl asked, seriousness in her voice. The boy smirked, amused with how serious she was trying to act._

 _"Does it matter?" The boy asked, and the girl nodded quickly so he continued, "If you become my ally, I shall tell you."_

 _The girl tilted her head slightly, "A-ally? You mean like a friend?"_

 _The boy thought, then nodded, allies were ALMOST like friends._

 _The girl shrugged and said, "W-well.. sure I guess.." The boy smiled, pleased with her answer._

 _"So," She started, "Who am I?"_

 _The boy smiled and said, "..Kry-Emiko, Emiko Setsuko."_

 _The girl, Emiko, smiled and said, "Oooh! That's a cool name! I like it!" The girl then stared confusedly at the place around her._

 _"So.. where are we?" Emiko asked, turning around and inspecting the area._

 _"We are on Earth, but we are going to attend a school called, Kadic Academy." The boy informed, but the girl turned back to him, asking, "Why?"_

 _"Because you know what they say, 'keep your friends close, but enemies closer." He replied._

 _Emiko played with her fingers and asked, "Who are our enemies? And who are you?"_

 _He waved his finger infront of her face, "Nu-huh, I'm not telling you are enemies just yettt."_

 _"But, " He put his finger down and stared seriously at her, "I am XANA. Welcome to my team."_

* * *

 **Author's note: SO! What do you think? Good, bad? Should I rewrite it? Give me your opinions!**

 **Enjoy! ^_^**


	2. Chapter 1

**Author's note: YAY! Chapter 1! I Hope you all enjoy, okay? ^-^**

 **Also, sorry if this chapter is a little short too, I'm trying to get my own ideas instead of basing it off the show, but I'll have to get use to it, so this chapter may be a little shorter than what they normally are.**

* * *

"Krystal, no!" Aelita screamed, quickly panting.

"Oh.. it's just a dream.." Aelita muttered. Suddenly, there was a knock on the door and it was a female's voice asking, "Hey? Are you okay in there?" Aelita blushed in embarrassment, realizing that she probably woke up everyone in the girls' dorm building. Aelita steadily walked over to the door to reveal Stella, and a couple other girls.

"Yea I'm fine, sorry, it was just a nightmare." Aelita apologized and Stella, along with all the other girls outside their dorms, nodded and went back inside to go to sleep. Aelita sighed as she closed the door and looked at the empty bed where Krystal used to sleep.

 **~~~~The Next Morning~~~~**

"Even though XANA is gone, my nightmares are getting worse and worse." Aelita said, drinking some hot coco as all the Lyoko Warriors were gathered around the dispenser machine(I never know what to call it! Ugh!)

"What was it about this time?" Ulrich asked, grabbing a soda from the dispenser machine.

"This time, " Aelita took a sip of her hot coco, "It was about Krystal this time, I just.."

Yumi looked at Aelita sympathetically. Odd also looked down and said, "We all still miss her.."

William walked up to all of them smiling and asking, "Hey guys, did you hear about the two new transfer students?"

The warriors looked at William, slightly confused with what he was saying, William, noticing this, explained, "It says it right there in the paper, 'Two new transfer students coming all the way from Fuji, Japan.'"

Ulrich picks up a school paper and starts reading it, saying, "He's right! Hey, that's pretty cool!"

"I bet Yumi would get along great with them, then." Odd teased, and Yumi raised her eye-brow at him.

"Just because I'm Japanese doesn't mean I always wanna be around them." She told and Odd shrugged. William stopped and commented, "Oh, Yumi, by the way, I love your new haircut."

Yumi smiled at him, simply replying, "Thanks." He nodded his head, smiling back at her. Ulrich slightly frowned, jealousy filling in him. When the bell rang, they all waved goodbye to eachother, going their separate ways.

When Odd and Ulrich were walking, Odd bumped into a girl with blue hair.

"Oh sorr- Woah! Awesome hair! Are you new here?" Odd commented, and the girl smiled at him, replying, "Yes, I transferred here, along with my brother."

"You're the girl who transferred from Fuji, Japan, right?" Odd asked, and the girl nodded in response.

"My name is Emiko Setsuko, what's your name?" The blue haired girl, Emiko, asked Odd.

Odd smiled at her and replied, "The names, Odd, Odd Della Robbia, and this is my pal, Ulrich Stern."

Emiko waved at Ulrich, who waved back and suddenly a blonde haired came up from behind Emiko informing, "Emi, we've got to get going."

Emiko turned to him and smiled, then turned back to Odd and Ulrich saying, "This is my older brother, XA-"

her 'brother' her cut off, saying, "I'm Yoru Setsuko, it's a pleasure to meet." Yoru slightly bowed before grabbing Emiko's arm and walking off.

"Emiko, I told you to call me Yoru." Yoru whispered in a warning voice, and Emiko quickly apologized for her mistake. Ulrich and Odd looked at the siblings weird, before forgetting that they came from Japan, so their culture is going to be different.

 **~~~~In Math Class~~~~**

Yumi looked out the window, her and William were sharing a table right next to the window. Suddenly, there was a knock on the door and the teacher said, "Come in!" Two new students appeared, one with blue hair and one with blonde.

Students just stared at the two new students in awe, whispering at how 'charming' the boy was and how 'cute' the girl was.

"Ah! Our two new students! Why don't you introduce yourselves?" The teacher asked, and Emiko slightly nervously glanced at her brother.

"My name is Yoru Setsuko, and this is my sister, Emiko Setsuko, " He looked at the crowd of students, putting on a charming smile and saying in a seductive voice, " _It's nice to meet you, new **friends.**_ " He said that, especially looking at Yumi, who gave him a half smile back.

"Alright, now, there are two seats right over there." The teacher pointed to a vacant table, that was right behind Yumi and William.

 _Great, just my luck,_ Yumi thought, sneering at herself in thought. The teacher then started to write an equation on the board.

 _"_ Excuse me.." Emiko whispered, slightly poking Yumi.

"Yea?" Yumi replied, turning to Emiko.

"I'm sorry but, I dropped my pencil under your chair.. would it be okay if you got it for me..?" Emiko asked, Yumi nodded and grabbed Emiko's blue mechanical pencil. Emiko muttered a 'thanks' before going back and paying attention to what the teacher said.

"Alright then! Can anyone tell me the multiple of X if Z equals 24,000?" The teacher asked, and the whole class was staring like 0-0. _Ugh, this is Jeremy homework, I wish he was in my class right now,_ Yumi thought, sighing as she saw none of the students raising their hands.

Yoru then raised his hand and the teacher called on him, making him answer, "If Z equals 24,000 than the multiple of X would be 6,000, but since it does not give us enough information, we can't make an exact answer."

The teacher and class stared at him, most of the girls gossiping and whispering about how 'charming' and 'smart' he was. Yumi too, stared at him in shock, it was a very difficult equation, and Yumi is almost the smartest kid in her class. She didn't really mind the Emiko girl, Emiko seemed like a nice girl to Yumi, but something was not right with Yoru to Yumi, something about him seems dangerous to her.

"U-huh.. c-correct.." The teacher stuttered, looking through her math book, she then closed it and looked directly at him, "But please stay with the flow of the class, don't jump ahead next time."

"You are right, I am truly sorry." Yoru politely said, giving another charming smile and making half of the girls swoon over him. William slightly sneered, whispering to Yumi, "He can't be a flirt! That's my job!"

Yumi rolled her eyes at him, retorting, "Yea but he seems to be doing a better job, atleast he's actually cute." Yumi then blushed slightly at what she had just said, making William frown slightly at her before turning away.

"Get over yourself William, " Yumi turned to him, "I was just jok-"

"Ms. Ishiyama, is there something you'd like to say to the class?" The teacher asked, Yumi looked up, embarrassed and shaking her head in response.

"Good." The teacher said, slightly glaring at Yumi before turning back to her board.

 _BRING, BRING!_ The school bell went, indicating that math class was now over and it was time for lunch. Everyone got up and grabbed their backpacks and book bags, heading towards the door.

"Ishiyama?" Emiko asked and Yumi turned around to see Emiko walk up to her and William.

"Thank you again for picking up my pencil." She thanked, slightly bowing and walking out the door.

"And she's Japanese?! She's way too nice! I thought all Japanese people were as cold as you, Yumi (A/N: No offence to anyone Japanese!)." William thought aloud and Yumi glared at him, slightly defended, then impressed.

"Wow, you actually just offended me." Yumi said, shocked as they headed towards the cafeteria.

William only shrugged and said, "Maybe I've moved on." Yumi raised her eye brow, asking, "Moving on to who?"

William blushed, not bothering to reply. Yumi only stared at him questioningly, before shrugging it off and continue walking with him to the cafeteria. They both walked up to the door to see girls surrounded by Yoru and a nervous looking Emiko.

"Watashi wa Kowaii desu..(I'm scared..), Tabetaidesu(I want to eat). " Emiko spoke in Japanese, Yumi, understanding what she just said, slightly felt bad for Emiko, Emiko didn't really seem the type to like to be around anyone, to Yumi anyways.

"Ii-desu, ii-desu(Alright, alright.)" Yoru spoke, winking at some of the girls, who had hearts in their eyes.

 _"Wow! That's so cool you guys can speak Japanese!"_

 _"Yea it is! Hey, isn't there another girl who can speak Japanese?"_

 _"I think so.. like Ishinama.. I think."_

 _"I think her first name was Yuri.. or was it Yoona?"_

 _"No! I think it was Yumi, right?"_

The girls spoke endless chatter, while they were distracted, Yumi saw Yoru and Emiko slip away from the crowd and into the food line. Bravely, Yumi walked behind them, with William following.

"Hey.. Emiko.. was it?" Yumi asked, as they were all getting their food, Emiko turned around, smiling and nodding.

"Ah! Ishiyama!" Emiko gasped, remembering the girl who gave her pencil back to Emiko.

"Actually it's Yumi.. Ishiyama is my last name." Yumi informed and Emiko nodded, apologizing for her mistake.

"This is my friend, William." Yumi introduced William, who was behind her.

"Yo!" He greeted and she waved back at him. Yoru noticed the three conversing, he slightly frowned, but covered it up with a smile and spoke, "It's nice to meet you both, my name is Yoru."

Yumi and William nodded in response, saying 'hi's' and 'yo's'.

"We have more friends, wanna sit with us?" Yumi asked, Emiko smiled brightly and said, "Su-"

Yoru jumped infront of her and responded, "You are so kind, _Yumi!_ But, unfortunately, we are a bit busy, with exploring the school and all." Yumi nodded, understanding, but Emiko turned to Yoru and slightly pouted.

Once they got their food, Yoru waved at Yumi and William and grabbed Emiko's hand, and the two walked out of the cafeteria, with some girls still gossiping and talking about them.

* * *

 **(Emiko's P.O.V)**

"Aw! I really wanted to hang with them..." I said, really disappointed, you see, XANA.. wait no _Yoru,_ wanted me to stay close to him at all times, and since we are 'allies', he wants me to be in his eye sight, AT ALL TIMES. Honestly, XA-no-Yoru, is not that bad of a person, but he's a bit too bossy.

"I understand, but we have to, no, you have to stay away from them, got it?" Yoru asked me, narrowing his eyes at me. Honestly, I don't know what's so important about staying away from them. I crossed my arms and put a pout on my face, hoping that'll make Yoru let me hang around them. Really, they seemed like nice people.

"Tsk, tsk, I don't fall for that Emi~chan!" Yoru sang in a sweet-sickening voice, I've only known Yoru for about 4-6 hours I think, but I can already tell when he's annoyed, which is apparently a lot.

"Then explain why I can't be around them?!" I slightly raised my voice. Normally, I don't really do that, but at this moment, I feel it's necessary. Yoru once again narrowed his eyes at me, though to be honest, it did slightly scare me.

"Never mind... never mind." I brushed off, he nodded, obviously happy with what I just said. We sat down on a step, near the entrance of a forest and began to eat our food.. finally.

"We've met some of the warriors already.. phase 1 is done, now we must move on to phase 2.." Yoru mumbled to himself, wait.. we met the warriors already?! When?! Where?! I looked up at Yoru and asked, "When did we meet them?"

Yoru sighed and muttered to himself, "I can't keep this much longer from you, can I?" I giggled slightly, finally! He'll tell me what's going on and who the warriors are and.. stuff.

"The Lyoko Warriors are, Yumi Ishiyama, my ex faithful servant- William Dunbar, Aelita Stones, Ulrich Stern, Odd Della Robbia and Jeremy Belpois, they are our enemies." Yoru explained, Ishi-YUMI?! But.. she's so nice and so was that William dude.. So that's why Yoru didn't want me around them.. OH.

"Do you understand?" Yoru asked, I nodded in response.

He sighed, "Great phase 3 is already knocked out of the way... but we still need to do phase 2."

I looked up and stared at Yoru in confusion, he made phases?! Since when?! Atleast, I've never heard of his plan and I'm his ALLY! He's not that great of a partner.. as you could already tell..

"What is phase 2.. anyways?" I slowly asked, and Yoru smiled at me. Only.. it wasn't one of those charming smiles he would give to the girls of this school, it was a bit of an evil smile.. or sinister.. I don't even know.

"Phase 2 is, taking action." Yoru said evilly.

...

...

...

"What? Speak English." I asked, what is up with Yoru and trying to make things a cliff hanger or something?!

Yoru sighed and explained, "When I say 'taking action' I mean, now, we are going to progress in getting rid of them!"

Ohhh. That makes sense! I think.. "Oh!" I simply say, not really wanting to say anything else. We continued to finish eating our food before next class, this is going to be a LOONGG day!

* * *

 **Author's note: Again, so sorry that this chapter was really short! And my updates may be coming in slow from now on, but I am looking to completing this story, if 'm not too busy.**

 **Anyways, chapter 2 may take longer, because I haven't really written it yet, most of my chapters in my first story were pre-written. But not these, so once again, updates will be slow.. I'm not really good at predicting though.**

 **Anyways... Enjoy! ^-^**


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